Genome-Wide Resequencing Reveals High Connectivity and Localized Adaptive Signals in Manila Clam (Ruditapes philippinarum) Populations Along the Southeastern Coast of China

The Manila clam (Ruditapes philippinarum) is an economically important bivalve widely cultured in coastal aquaculture systems of China. However, the genome-wide genetic background and germplasm differentiation of geographically distinct populations remain unclear, which constrains germplasm conservation and the development of selective breeding programs. In this study, 50 individuals from five representative coastal populations (QZ, ZZ, ZP, CL, and NH) in China were subjected to whole-genome resequencing, producing 126.67 Gb of clean data and 92,593,087 SNPs after stringent filtering. Genetic diversity analyses showed that nucleotide diversity (π) ranged from 0.2453 to 0.2588, observed heterozygosity (Ho) from 0.1316 to 0.1492, and expected heterozygosity (He) from 0.2303 to 0.2435, with the CL population exhibiting relatively lower diversity. Population differentiation was low to moderate, with pairwise FST values ranging from 0.0454 to 0.0557. Principal component analysis, neighbor-joining phylogenetic analysis, and Admixture clustering consistently indicated limited population structure and extensive genetic admixture. TreeMix analysis further revealed directional gene flow among populations. Rapid linkage disequilibrium decay and predominantly positive Tajima’s D values suggested relatively stable demographic histories. Despite low genome-wide differentiation, combined FST and nucleotide diversity ratio analyses identified localized selective sweep signals in specific genomic regions. These results provide preliminary genome-wide insights into genetic diversity, population connectivity, and candidate localized differentiation signals in R. philippinarum. Given the low sequencing depth, the findings should be interpreted as population-level observations that require further validation using higher-depth genomic datasets before being applied to germplasm conservation and selective breeding programs.